This invention pertains generally to the field of biology and particularly to techniques and apparatus for the manufacture of DNA molecules of defined or desired sequences. The manufacture of DNA molecules also makes possible the synthesis of any desired peptides, proteins or assemblies of proteins and nucleic acids as may be desired.
Using the techniques of recombinant DNA chemistry, it is now common for DNA sequences to be replicated and amplified from nature and for those sequences to then be disassembled into component parts which are then recombined or reassembled into new DNA sequences. While it is now both possible and common for short DNA sequences, referred to a oligonucleotides, to be directly synthesized from individual nucleosides, it has been thought to be generally impractical to directly construct large segments or assemblies of DNA sequences larger than about 400 base pairs. As a consequence, larger segments of DNA are generally constructed from component parts and segments which can be purchased, cloned or synthesized individually and then assembled into the DNA molecule desired.
For example, if an expression vector is desired to express a new protein in a selected host, the scientist can often purchase a generic expression vector from a molecular biology supply company and then clone or synthesize the protein coding region for the gene sought to be expressed. The coding region must be ligated into the vector in such a manner and in the correct location and orientation such that the vector will be effective to express the desired protein in the host. The purchaser of the vector must also examine the sequence of the vector to make sure no other DNA component of the vector has other properties that might be detrimental to the experiment the purchaser wishes to run. Thus, the difficulty in constructing any new desired larger DNA construct is dependent on what similar constructs, or what components of the construct, can be purchased or obtained from public sources, and how much information is available about the sequences of those components.
Tools for genetic analysis are being developed to provide mechanisms to answer questions like these. Among such useful tools are what has become known as a DNA microarray. A DNA microarray is an array of different DNA strands arranged in an orderly fashion on a substrate. The DNA strands are organized into groups on the substrate, each individual group being called a feature. Ideally, all of the DNA strands in a single feature are identical in DNA sequence, and each of the different features can have an independent set of DNA strands of a different sequence from those in other features. It is a chemical trait of DNA that when single stranded DNA molecules are in solutions together at moderate or low temperatures, DNA strands of complementary sequence will spontaneously hybridize together through the formation of hydrogen bonds to form double stranded DNA. Thus a DNA microarray can be used to analyze a sample of unknown DNA (which has been made single stranded) to determine if complementary sequences are present in the sample simply by washing the unknown DNA sample over a microarray, and looking for the presence of double stranded DNA. DNA from the sample will hybridize to the array only when the sequence of the DNA from the sample matches the sequence in that particular feature. Thus, by intelligently designing and constructing DNA microarrays, which can contain thousands of these features in a single array, it becomes possible to rapidly gather large amounts of information about the DNA contained in a sample in a simple process. DNA microarrays are currently used mainly, and perhaps exclusively, for analytical purposes. Microarrays of DNA can be used for DNA sequencing, for the analysis of DNA from tissue samples, to identify individuals or to diagnose disease conditions and to study the tissue specific expression of native genes in any host.
To make a microarray of DNA strands, one can make a series of DNA strands and then place them on a support, or one can build DNA strands in situ covalently attached to the support. Both of these techniques have been used in the art to make microarrays. The first technique, sometimes referred to as spotting or gridding, is convenient for the rapid and convenient creation of novel or small quantity custom arrays since the capital cost of making the DNA strands is not large. The spotting strategy can, however, be limited in the density of the array that can be created due to the physical limitations of droplets of liquids containing DNA that can be deposited on a surface. The spotting strategy can also be error prone because of the need to keep strictly separate and properly identified hundreds or thousands of different oligonucleotides. The strategy of creating DNA strands in situ on a surface permits the manufacture of arrays in which each feature of the array is very small and in which there are very many features in a single array. Depending on the technique by which the DNA strands in the array are synthesized, however, the costs of making customized arrays can be quite high.
A technique has been described for the in situ synthesis of DNA microarrays that is adapted for the manufacturing of customized arrays. Published PCT patent application WO99/42813 and U.S. Pat. No. 6,375,903 describe a method for making such arrays in which the light is selectively directed to the array being synthesized by a high density micromirror array under software control from a computer. Since the micromirror array is operated totally under software control, the making of complex and expensive photolithographic masks is avoided in its entirety.